SuperScript IV Reverse Transcriptase as a better alternative to AMV-based enzymes

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1 WHITE PAPER SuperScript IV Reverse Transcriptase SuperScript IV Reverse Transcriptase as a better alternative to AMV-based enzymes Abstract Reverse transcriptases (RTs) from avian myeloblastosis virus (AMV) and Moloney murine leukemia virus (MMLV) are commonly used in research to synthesize complementary DNA (cdna) from RNA templates. MMLV RT based enzymes were traditionally the preferred choice due to several desirable attributes such as lower RNase H activity, ability to synthesize longer cdnas, and higher fidelity. AMV RT based enzymes, including engineered AMV RTs such as Invitrogen ThermoScript RT, were often recommended in applications requiring higher thermostability than the original generation of MMLV-derived RTs could support. Invitrogen SuperScript IV RT is a new-generation MMLV-based RT that has been engineered for further thermostability and processivity, and as with all enzymes in the Invitrogen SuperScript family, reduced RNase H activity. Using a variety of assays, this study demonstrates that SuperScript IV RT offers advantages at standard as well as elevated temperatures over cloned AMV and ThermoScript RT, including higher sensitivity, inhibitor tolerance, and ability to work with degraded RNA. Researchers currently using AMV-based RTs in their protocols are encouraged to use as a replacement. Introduction RTs are DNA polymerases that synthesize cdna from an RNA template. They are widely used to study gene expression in research samples, such as tissues and cells, and more recently in single-cell analysis and next-generation sequencing (NGS) applications. RTs are characterized by several attributes (Table 1). Enzyme processivity describes the number of nucleotides incorporated during a single binding event of an RT to a primed template before dissociation. High processivity is a key enzyme feature and results in additional desirable attributes such as higher efficiency, shorter reaction time, higher tolerance to inhibitors, and higher thermostability. High RT thermostability allows cdna synthesis to be performed at elevated temperatures (at or higher), which helps denature regions of strong RNA secondary structure for longer cdna and higher yields [1,2]. Table 1. Key performance attributes of different RT enzymes. MMLV RT AMV RT Processivity 1,500 nt 30 nt 400 nt 400 nt Reaction temperature Up to Up to 42 C Up to Up to Reaction time 10 min 60 min 60 min 60 min RNase H activity Relative cdna yield* Not detectable Medium High Low High Low Medium Medium Fidelity * cdna yields from samples including challenging or low-purity RNA.

2 In addition to DNA polymerase activity, RTs also possess RNase H endonuclease activity that cleaves the RNA template in an RNA DNA duplex and often limits full-length cdna synthesis [3]. Engineered RT variants with reduced endonuclease activity, termed H-minus RTs, are often preferred because of improved performance in synthesizing longer cdna [4 6]. Commercially available RTs used in molecular biology are generally derived from MMLV or AMV. and engineered variants of AMV RT (e.g., ) were often used when success of RT reactions depended on higher temperatures than wild type MMLV RT could withstand. In their wild type forms, AMV RTs demonstrate higher processivity at approximately 400 nucleotide additions per binding event, compared to 30 nucleotides for MMLV RT [1,2,7,8]. Newer research applications and use of increasingly difficult sample types in molecular biology research demand superior RTs that not only are highly processive and thermostable, but also demonstrate high inhibitor tolerance, high sensitivity, lower error rate, and shorter reaction times., the newest member of the SuperScript family, is an engineered MMLV RT designed for superior performance even with challenging RNA samples. has significantly better processivity compared to other MMLV and AMV RTs, as well as increased thermostability, resistance to inhibitors, and sensitivity [9]. As with all enzymes in the SuperScript family, has reduced, undetectable RNase H activity. In this study we tested the performance of SuperScript IV RT, cloned AMV RT, and at standard and high reaction temperatures (up to ) with RNA of low input, suboptimal purity, or poor quality. The data demonstrate that offers better performance than cloned AMV and s under the conditions tested. Materials and methods Commercial RNA samples Commercial RNA samples used included HeLa S3 total RNA (component of Ion Total RNA-Seq Kit v2, Cat. No ), Invitrogen Human Placenta Total RNA (Cat. No. AM7950), and Invitrogen Kb RNA Ladder (Cat. No ). Generation of degraded RNA 1 µg each of Human Placenta Total RNA and HeLa S3 total RNA were degraded to an RNA integrity number (RIN) of 2.6 and 1, respectively, by addition of MgCl 2 to 1 mm final concentration and incubation at 95 C for 15 minutes. RIN was evaluated using an Agilent 2100 Bioanalyzer system and Agilent RNA 6000 Nano Kit. cdna synthesis protocol The Invitrogen SuperScript IV First-Strand Synthesis System (Cat. No ), Invitrogen Cloned AMV First-Strand cdna Synthesis Kit (Cat. No ), and Invitrogen ThermoScript RT-PCR System for First-Strand cdna Synthesis (Cat. No ) were used according to their standard protocols, unless otherwise specified. For all experiments, oligo(dt) 20 primers were used. To visualize synthesized cdna using Kb RNA Ladder as a template, reactions were resolved by alkaline gel electrophoresis and stained with Invitrogen SYBR Gold Nucleic Acid Gel Stain (Cat. No. S11494). qpcr qpcr was performed on the reverse transcription samples using Thermo Scientific Luminaris Probe qpcr Master Mix, Low ROX (Cat. No. K0944) with the Applied Biosystems TaqMan Assays indicated in the figures. Reverse transcription reactions made up 10% of the total 20 µl qpcr reaction volume. Assays were performed on an Applied Biosystems 7500 Fast Real-Time PCR System. For the inhibitor assays, ΔC t was calculated as (C t inhibitor C t control). Endpoint PCR The reverse transcription reactions contributed 4% of the total PCR reaction volume. Invitrogen Platinum Taq DNA Polymerase High Fidelity (Cat. No ) was used for PCR amplification using its recommended protocol on an Applied Biosystems ProFlex PCR System. 8 μl of PCR reaction was resolved using agarose gel electrophoresis in TAE buffer and visualized by ethidium bromide staining.

Results and discussion Ability to work at increased temperatures Thermostable RT enzymes allow reactions to be performed at higher temperatures, which helps denature regions of strong RNA secondary

High RT thermostability is a consequence of high processivity, which in turn allows synthesis of long, full-length cdna in less time [1].

3 Results and discussion Ability to work at increased temperatures Thermostable RT enzymes allow reactions to be performed at higher temperatures, which helps denature regions of strong RNA secondary structure that can otherwise cause RTs to stall and limit cdna size. High RT thermostability is a consequence of high processivity, which in turn allows synthesis of long, full-length cdna in less time [1]. The thermostability of RTs and their ability to synthesize fulllength cdna were compared using 1 µg of Kb RNA Ladder template with oligo(dt) 20 primers at temperatures between 45 and. was tested at reaction times of 10, 30, and 60 minutes (10 minutes is the recommended reaction time), while cloned AMV and s were tested at 30 or 60 minutes. Figure 1 shows that synthesized up to 10 kb cdna in only 10 minutes, even at. was able to synthesize the largest cdna fragment at 60 minutes at all temperatures, while cloned AMV RT was able to synthesize up to 10 kb cdna in 60 minutes at, but only up to 6 kb at. The same results were observed for the 30-minute reverse transcription reactions (data not shown). These results demonstrate that due to its exceptional processivity and enhanced thermostability, was able to synthesize large, full-length cdna fragments in 10 minutes, even at challenging reaction temperatures. Other enzymes require more time for cdna synthesis or don t perform as well at the highest temperatures. Kb min 60 min 60 min 60 min Figure 1. Ability to synthesize cdnas of different lengths at a range of temperatures and reaction times using, AMV RT, and. Performance in the presence of inhibitors Numerous compounds that have inhibitory effects on RTs are commonly found in RNA samples, even after employing thorough purification methods [9,10]. Some examples of inhibitory compounds include phenol from Invitrogen TRIzol Reagent that is used to extract RNA from cells and tissues, and salts such as guanidine that is used in multiple steps during RNA isolation. RT inhibitors may also be inherent in the biological sample source: hematin from blood, bile salts from blood and feces, and humic acid from soil and thus, from plants. To test how different compounds affect RT enzymes, cdna synthesis was performed using 100 ng of total HeLa RNA in the presence of individual inhibitors at final concentrations indicated in Figure 2 in optimal () as well as challenging () reaction conditions. At, the reaction time was the recommended 10 minutes for and 60 minutes for cloned AMV and s. At, the reaction time was 60 minutes for all three enzymes. qpcr was performed with TaqMan Assays for ACTB and GUSB targets.

4 Figure 2 shows the ΔC t value between the inhibitorcontaining and control RT-qPCR reactions for each sample. In almost all conditions tested, ΔC t values for SuperScript IV RT were lower than ΔC t values for cloned AMV and s, confirming that has better inhibitor tolerance. The improvement is especially pronounced at the challenging reaction temperature ACTB, cdna synthesis sensitivity High sensitivity, or the ability of RTs to generate cdna from very little input RNA, is an important attribute of this class of enzymes, especially as researchers increasingly work on smaller RNA input. The sensitivity of the three RTs was tested by performing two-step RT-PCR with 1 µg down to 1 pg of total HeLa RNA input at and. At, the reaction time was 10 minutes for and 60 minutes for AMV and s. At, all three RTs were tested using a 60-minute reaction time. The synthesized cdna was then amplified by endpoint PCR using Platinum Taq DNA Polymerase High Fidelity with primer pairs for ACTB (356 bp), LAM (997 bp), and ACTR (3,009 bp) targets. PCR products were resolved by agarose gel electrophoresis and visualized by ethidium bromide staining (Figure 3). ACTB, 1 µg 100 ng 10 ng 1 ng 100 pg 10 pg 1 pg 1 µg 100 ng 10 ng 1 ng 100 pg 10 pg 1 pg 1 µg 100 ng 10 ng 1 ng 100 pg 10 pg 1 pg ACTB LAM GUSB, ACTR Figure 3. Sensitivity of, AMV RT, and. GUSB, Figure 2. Two-step RT-qPCR performance using, AMV RT, and in the presence of inhibitors (ΔC t = C t inhibitor C t control).

5 In each case, showed the highest sensitivity, producing a detectable product at 10- to 100-fold lower input RNA than the other two RTs (Figure 3). At both the optimal temperature and the challenging temperature, outperformed AMV RT and for all three targets. The ability to detect longer targets, such as ACTR, indicates that the reduced RNase H activity and improved thermostability of allows it to synthesize more full-length cdna. Performance with degraded RNA samples Researchers are working with increasingly difficult sample sources where RNA becomes degraded during the purification process. SuperScript IV RT, cloned AMV RT, and performance was evaluated using degraded total HeLa RNA (RIN 1) and human placenta RNA (RIN 2.6) at and. At, the reaction time was 10 minutes for and 60 minutes for cloned AMV and s. At, the reaction time was 60 minutes for all three enzymes. cdna was used for qpcr with TaqMan Assays for 18S rrna, GAPDH, HPRT1, and TBP targets (Figure 4). Ct Ct Human placenta RNA (RIN 2.6) HeLa S3 total RNA (RIN 1) S rrna GAPDH HPRT1 TBP 18S rrna GAPDH HPRT1 TBP Figure 4. Performance of, AMV RT, and with degraded RNA templates. For all conditions tested, produced the highest cdna yields and the lowest C t values. Additionally, the C t values for SuperScript IV RT at were nearly identical to their values at the optimal (ΔC t < 1), whereas the performance of the other two products was substantially worse at the higher temperatures, with C t values between 1.5 and 8 cycles higher than at the optimal temperature. These results demonstrate the superior sensitivity, thermostability, and overall performance of with degraded RNA. Conclusion As research moves toward challenging samples and applications and demands on reverse transcriptases increase, enzyme performance must keep pace. While AMV-derived RTs used to have a thermostability advantage over wild type MMLV RT, the technology has evolved, and better MMLV RT based enzymes are available. Thermo Fisher Scientific has engineered, an MMLV RT based enzyme with significantly improved processivity (50-fold higher than wild type MMLV RT, SuperScript II RT, and SuperScript III RT, and 3-fold higher than AMV RT and ). outperforms other RTs, especially under challenging reaction conditions at temperatures up to, in the presence of inhibitors, and with degraded RNA. In addition, reactions with are faster and more sensitive. Researchers can confidently replace AMV RT or in their current protocols with

6 References 1. Gerard GF et al. (2002) The role of template-primer in protection of reverse transcriptase from thermal inactivation. Nucleic Acids Res 30: Harrison GP et al. (1998) Pausing of reverse transcriptase on retroviral RNA templates is influenced by secondary structures both 5 and 3 of the catalytic site. Nucleic Acids Res 26: Champoux JJ et al. (2009) Ribonuclease H: properties, substrate specificity and roles in retroviral reverse transcription. FEBS J 276: Kotewicz ML et al. (1988) Isolation of cloned Moloney murine leukemia virus reverse transcriptase lacking ribonuclease H activity. Nucleic Acids Res 16: Tanese N et al. (1988) Domain structure of the Moloney murine leukemia virus reverse transcriptase: mutational analysis and separate expression of the DNA polymerase and RNase H activities. Proc Natl Acad Sci USA 85: Gerard G et al. (1997) Reverse transcriptase. The use of cloned Moloney murine leukemia virus reverse transcriptase to synthesize DNA from RNA. Mol Biotechnol 8: Baranauskas A et al. (2012) Generation and characterization of new highly thermostable and processive M-MuLV reverse transcriptase variants. Protein Eng Des Sel 25: DeStefano JJ et al. (1991) Polymerization and RNase H activities of the reverse transcriptases from avian myeloblastosis, human immunodeficiency, and Moloney murine leukemia viruses are functionally uncoupled. J Biol Chem 266: SuperScript IV Reverse Transcriptase. White paper available at thermofisher.com (Pub. No. COL03257). 10. Schrader C et al. (2012) PCR inhibitors occurrence, properties and removal. J Appl Microbiol 113: Ordering information Product Quantity Cat. No. 2,000 units SuperScript IV Reverse Transcriptase 10,000 units x 10,000 units SuperScript IV First-Strand Synthesis System SuperScript IV VILO Master Mix SuperScript IV VILO Master Mix with ezdnase Enzyme 50 reactions reactions reactions reactions reactions reactions Find out more at thermofisher.com/ssiv For Research Use Only. Not for use in diagnostic procedures Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. TaqMan is a registered trademark of Roche Molecular Systems, Inc., used under permission and license. Agilent and Bioanalyzer are trademarks of Agilent Technologies, Inc. COL

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